1I12 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA

Authors :   C. Peneff, D. Mengin-Lecreulx, Y. Bourne

Date :   30 Jan 01 (Deposition) - 16 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Gnat, Alpha/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Peneff, D. Mengin-Lecreulx, Y. Bourne
The Crystal Structures Of Apo And Complexed Saccharomyces Cerevisiae Gna1 Shed Light On The Catalytic Mechanism Of An Amino-Sugar N-Acetyltransferase.
J. Biol. Chem. V. 276 16328 2001
PubMed-ID: 11278591 | Reference-DOI: 10.1074/JBC.M009988200
(for further references see the PDB file header)

Molecule 1 - GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
	Chains	:	A, B, C, D
	EC Number	:	2.3.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15 (PREP4)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YFL017C
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PHOSPHOGLUCOSAMINE TRANSACETYLASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACO	4	Ligand/Ion	ACETYL COENZYME *A
2	IMD	2	Ligand/Ion	IMIDAZOLE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACO	2	Ligand/Ion	ACETYL COENZYME *A
2	IMD	1	Ligand/Ion	IMIDAZOLE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	ACO	2	Ligand/Ion	ACETYL COENZYME *A
2	IMD	1	Ligand/Ion	IMIDAZOLE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:141 , ACO A:1201 , HOH A:1210 , LEU B:27 , ASP B:99 , ILE B:100 , ALA B:101 , VAL B:102 , GLN B:107 , GLY B:108 , GLN B:109 , GLY B:110 , LEU B:111 , GLY B:112 , LYS B:113 , ASP B:134 , ASN B:139 , PHE B:142 , TYR B:143 , LYS B:145 , HOH B:1201 , HOH B:1238 , HOH B:1243 , HOH B:1247 , HOH B:1249 , HOH B:1250 , HOH B:1259 , HOH B:1266 , HOH B:1298 , HOH B:1306 , THR D:29	BINDING SITE FOR RESIDUE ACO B 1200
2	AC2	SOFTWARE	VAL A:26 , LEU A:27 , ASP A:99 , ILE A:100 , ALA A:101 , VAL A:102 , GLN A:107 , GLY A:108 , GLN A:109 , GLY A:110 , LEU A:111 , GLY A:112 , LYS A:113 , ASP A:134 , ASN A:139 , LYS A:141 , PHE A:142 , TYR A:143 , LYS A:145 , HOH A:1202 , HOH A:1228 , HOH A:1236 , HOH A:1249 , HOH A:1262 , HOH A:1263 , HOH A:1274 , HOH A:1286 , HOH A:1288 , HOH A:1306 , HOH A:1333 , HOH A:1378 , LYS B:141 , ACO B:1200	BINDING SITE FOR RESIDUE ACO A 1201
3	AC3	SOFTWARE	ASP C:99 , ILE C:100 , ALA C:101 , VAL C:102 , GLN C:107 , GLY C:108 , GLN C:109 , GLY C:110 , LEU C:111 , GLY C:112 , LYS C:113 , ASP C:134 , LYS C:138 , ASN C:139 , LYS C:141 , PHE C:142 , TYR C:143 , LYS C:145 , HOH C:1205 , HOH C:1249 , HOH C:1250 , HOH C:1258 , HOH C:1283 , HOH C:1298 , HOH C:1312	BINDING SITE FOR RESIDUE ACO C 1202
4	AC4	SOFTWARE	VAL D:26 , ASP D:99 , ILE D:100 , ALA D:101 , VAL D:102 , GLN D:107 , GLY D:108 , GLN D:109 , GLY D:110 , LEU D:111 , GLY D:112 , LYS D:113 , ASP D:134 , LYS D:138 , ASN D:139 , LYS D:141 , PHE D:142 , TYR D:143 , LYS D:145 , HOH D:1207 , HOH D:1253	BINDING SITE FOR RESIDUE ACO D 1203
5	AC5	SOFTWARE	ASP B:117 , VAL B:120 , HOH B:1258 , ILE D:157 , LYS D:159	BINDING SITE FOR RESIDUE IMD B 1001
6	AC6	SOFTWARE	ILE A:82 , HIS A:96 , ILE C:82 , HIS C:96 , HOH C:1270	BINDING SITE FOR RESIDUE IMD A 1002

(no "SS Bond" information available for 1I12)

(no "Cis Peptide Bond" information available for 1I12)

(no "SAP(SNP)/Variant" information available for 1I12)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	4	A:28-159 B:28-159 C:28-158 D:28-159

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	2	A:28-159 - C:28-158 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	2	- B:28-159 - D:28-159

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YFL017C	1	YFL017C.1	VI:104456-103977	480	GNA1_YEAST	1-159	159	4	A:3-159 (gaps) B:2-159 (gaps) C:1-158 (gaps) D:1-159 (gaps)	157 158 158 159

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:154
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
           GNA1_YEAST     3 LPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i12a_ A: Glucosamine-phosphate N-acetyltransfera   se GNA1                                                                                                  SCOP domains
               CATH domains 1i12A00 A:3-159  [code=3.40.630.30, no name define   d]                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh....---.........eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------GNAT  PDB: A:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 Exon 1.1  PDB: A:3-159 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                     Transcript 1
                 1i12 A   3 LPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWN---DKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                    12        22        32        42        52   |    62        72        82        92       102       112       122       132       142       152       
                                                                            52  56

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           GNA1_YEAST     2 SLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i12b_ B: Glucosamine-phosphate N-acetyltransferas    e GNA1                                                                                                  SCOP domains
               CATH domains 1i12B00 B:2-159  [code=3.40.630.30, no name defined    ]                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhh..ee..----..ee....eeeee.hhheeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GNAT  PDB: B:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-159 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                      Transcript 1
                 1i12 B   2 SLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWN----KKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                    11        21        31        41        51|    |  61        71        81        91       101       111       121       131       141       151        
                                                                             52   57

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                             1                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         
           GNA1_YEAST     - -MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i12c_ C: Glucosamine-phosphate N-acetyltransferase      GNA1                                                                                                  SCOP domains
               CATH domains 1i12C00 C:0-158  [code=3.40.630.30, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhh......-----....eeeeeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.......hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------GNAT  PDB: C:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 -Exon 1.1  PDB: C:1-158 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                      Transcript 1
                 1i12 C   0 SMSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWN-----KIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
                                     9        19        29        39        49  |     59        69        79        89        99       109       119       129       139       149         
                                                                               52    58

Chain D from PDB  Type:PROTEIN  Length:157
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           GNA1_YEAST     - -MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i12d_ D: Glucosamine-phosphate N-acetyltransferase GN   A1                                                                                                     SCOP domains
               CATH domains 1i12D00 D:0-159  [code=3.40.630.30, no name defined]                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhee....---.ee....eeeee.....eeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------GNAT  PDB: D:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 -Exon 1.1  PDB: D:1-159 (gaps) UniProt: 1-159                                                                                                                    Transcript 1
                 1i12 D   0 SMSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDN---KIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                     9        19        29        39        49    |   59        69        79        89        99       109       119       129       139       149       159
                                                                                 54  58

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: N-acetyl transferase, NAT (154)

Protein domain: Glucosamine-phosphate N-acetyltransferase GNA1 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1i12a_	A:
1b	d1i12b_	B:
1c	d1i12c_	C:
1d	d1i12d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Aminopeptidase (284)

Homologous Superfamily: [code=3.40.630.30, no name defined] (126)

Baker's yeast (Saccharomyces cerevisiae) (10)

1a	1i12D00	D:0-159
1b	1i12A00	A:3-159
1c	1i12B00	B:2-159
1d	1i12C00	C:0-158

(no "Pfam Domain" information available for 1I12)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GNA1_YEAST | P43577)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0004343	glucosamine 6-phosphate N-acetyltransferase activity	Catalysis of the reaction: D-glucosamine 6-phosphate + acetyl-CoA = N-acetyl-D-glucosamine 6-phosphate + CoA + H(+).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006048	UDP-N-acetylglucosamine biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.

Asymmetric Unit
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(no "Cis Peptide Bonds" information available for 1i12)

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	1i12
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	GNA1_YEAST \| P43577	:	1i1d 1i21

1i1d	CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P
1i21	CRYSTAL STRUCTURE OF YEAST GNA1

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